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ProteomicsProteome-Centric Cross-Omics Characterization and Integrated Network Analyses of Triple-Negative Breast Cancer
We undertook the first systemic proteomic study of a 90-case cohort of triple-negative breast cancer (TNBC) with a panoramic proteome view in quantification, phosphorylation, and DNA-binding capacity. Four integrative subtypes (iP-1-4) were stratified based on the proteome quantification profile and...
ORGANISM(S): Homo Sapiens 
2021-08-24 | PXD028102 |
TranscriptomicsLong-range chromosome interactions mediated by cohesin shape circadian gene expression [RNA-Seq]
Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes. As genome-wide transcription is organized under the high-order chromosome structure, it is unclear how circadian gene ...
ORGANISM(S): Mus musculus 
2016-04-04 | E-GEOD-68831 | biostudies-arrayexpress
GenomicsLong-range chromosome interactions mediated by cohesin shape circadian gene expression [ChIP-Seq]
Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes. As genome-wide transcription is organized under the high-order chromosome structure, it is unclear how circadian gene ...
ORGANISM(S): Mus musculus 
2016-04-04 | E-GEOD-77162 | biostudies-arrayexpress
TranscriptomicsEpigenetic silencing of Th1 chemokines shapes tumor immunity, immunotherapy and patient outcome [shEZH2]
To define the gene profile altered by EZH2 and H3K27me3 in response to IFNg, we performed several microarrays in primary ovarian cancer cells transfected with shEZH2 or treated with GSK126. We found that 155 and 124 genes were altered by shEZH2 and GSK126 treatment, respectively, and 20 genes were i...
ORGANISM(S): Homo sapiens 
2015-08-11 | E-GEOD-71870 | biostudies-arrayexpress
TranscriptomicsEpigenetic silencing of Th1 chemokines shapes tumor immunity, immunotherapy and patient outcome [GSK126]
To define the gene profile altered by EZH2 and H3K27me3 in response to IFNg, we performed several microarrays in primary ovarian cancer cells transfected with shEZH2 or treated with GSK126. We found that 155 and 124 genes were altered by shEZH2 and GSK126 treatment, respectively, and 20 genes were i...
ORGANISM(S): Homo sapiens 
2015-08-11 | E-GEOD-71869 | biostudies-arrayexpress
ProteomicsIdentification of an unrecognized circRNA associated with the development of renal fibrosis
In the current study, the RF model of the rat was established, and RNA-sequencing and real-time polymerase chain reaction (qRT-PCR) experiments were implemented. Subsequently, cell apoptosis and proliferation were carried out. Finally, the iTRAQ proteomics analyses were carried out for the samples.
ORGANISM(S): Homo Sapiens 
2022-10-31 | PXD037827 |
ProteomicsUltradeep N-glycoproteome Atlas of Mouse Reveals Spatiotemporal Signatures of Brain Aging and Neurodegenerative Diseases
The current depth of site-specific N-glycoproteomics is insufficient to fully characterize glycosylation events in biological samples. Herein, we achieved an ultradeep and precision analysis of the N-glycoproteome of mouse tissues by integrating multiple workflows. The largest N-glycoproteomic datas...
ORGANISM(S): Mus Musculus 
2025-03-04 | PXD061436 |
ProteomicsOLFM4 is a direct target of the cGAS-STING pathway and acts as an extracellular inhibitor for the Hippo signaling in EBV-associated cancer
To investigate protein components of MVs in EBVaGC, we collected clinical tissue samples of 3 EBV+ and 3 EBV- gastric cancer patients, and isolated MVs from these samples. Then performed 4D-label free quantitative proteomics analysis for each isolated MVs. Raw files of 6 samples are included in subp...
ORGANISM(S): Homo Sapiens 
2024-11-18 | PXD057977 |
ProteomicsA region-resolved mucosa proteome of the human stomach
The human gastric mucosa is the most active and functional layer that carries out food digestion and metabolic processes in physiological conditions and also the main origin of carcinogenesis in gastric cancer. Anatomically, the human stomach is divided into 7 regions with physiological functions, b...
ORGANISM(S): Homo Sapiens 
2018-11-26 | PXD011821 |
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